The acute and subacute toxicity of a newly synthesized silver selenide nanoparticles encapsulated in a natural polymeric matrix of arabinogalactan study has been studied. The nanocomposite is a promising material for the design of diagnostic and therapeutic drugs. It can also be used for the preparation of fluorescent labels and in thermal oncotherapy. The employment of binary nanocomposites enables one to unveil the potential hidden in metals which constitute these composites. The study of acute toxicity, carried out by the oral administration of nanocomposites at a dose of 2000 mg/kg, has shown that the compound belongs to low-toxic substances of the 5th hazard class. With the subacute oral administration of nanocomposites at a dose of 500 μg/kg, slight changes are observed in the brain tissue and liver of experimental animals, indicating the development of compensatory–adaptive reactions. In the kidneys, the area of the Shumlyansky–Bowman chamber decreases by 40.5% relative to the control group. It is shown that the application of the protective properties of selenium, which is contained in the composite, helps to reduce the toxicity of silver.